If she truely does not have a preference for any of the three bikes over the others, regarding comfort, then look at the specs of the bike.
First, gears, the Trek and Cannondale have the same gearing. I have the 7.3 and the gearing is much wider (11-32) and I can climb hills no problem. The Marin only has a 12 - 24 which is very very narrow, it will be very hard to climb any sort of incline with that gearing. For that reason I would kick the Marin out of the considerations. Or you could buy a new cassette if your girlfriend really likes that one. The shop would probably install it for free if you buy it with the bike.
The other difference is the fork, like you said. Have her ride the bikes and see if she notices any discrepencies in the shock absorbtion qualities of the carbon fiber over the aluminum. If she really can't tell any difference between the feel of the bikes, then go with the Trek.
The most important aspect is still how the bikes feels to her. If one bike is more comfortable than the others, then get that one.